Assembly-decontamination-VGP9

assembly-assembly-decontamination/main-workflow

Author(s)
Nadolina Brajuka
Version
1
Last updated
Sep 4, 2024
License
BSD-3-Clause
Tags
VGP_curated

Features
Tutorial
Decontamination of a genome assembly
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00284
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nScaffolded assembly fasta"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nDatabase for Kraken2"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["soft-masking "];
  0 -->|output| 2;
  3["hard-masking"];
  2 -->|outfile| 3;
  4["ID non-target contaminants"];
  1 -->|output| 4;
  3 -->|output| 4;
  c380857b-5180-4e82-a14f-8b575f10abaa["Output\nKraken2 classification scores"];
  4 --> c380857b-5180-4e82-a14f-8b575f10abaa;
  style c380857b-5180-4e82-a14f-8b575f10abaa stroke:#2c3143,stroke-width:4px;
  5["blast mitochondria DB"];
  3 -->|output| 5;
  6["Cut"];
  4 -->|output| 6;
  7["parsing blast output"];
  5 -->|output1| 7;
  1478af1e-52f4-48fe-b966-0a61e2014a58["Output\nmito_scaff_names"];
  7 --> 1478af1e-52f4-48fe-b966-0a61e2014a58;
  style 1478af1e-52f4-48fe-b966-0a61e2014a58 stroke:#2c3143,stroke-width:4px;
  8["Filter"];
  6 -->|out_file1| 8;
  64156e28-aaf0-4578-9a7e-d6d21774c2c8["Output\ncontaminants_table"];
  8 --> 64156e28-aaf0-4578-9a7e-d6d21774c2c8;
  style 64156e28-aaf0-4578-9a7e-d6d21774c2c8 stroke:#2c3143,stroke-width:4px;
  9["Cut"];
  8 -->|out_file1| 9;
  10["concatenate scaffold lists"];
  7 -->|mito_scaff_names| 10;
  9 -->|out_file1| 10;
  77084ec5-a145-40c1-9cfc-476d091105ae["Output\nfull contaminant + mito scaffold list"];
  10 --> 77084ec5-a145-40c1-9cfc-476d091105ae;
  style 77084ec5-a145-40c1-9cfc-476d091105ae stroke:#2c3143,stroke-width:4px;
  11["removing scaffolds "];
  0 -->|output| 11;
  10 -->|out_file1| 11;
  88a8e9ed-d92c-4340-aaad-c6d450a336aa["Output\nfinal decontaminated assembly"];
  11 --> 88a8e9ed-d92c-4340-aaad-c6d450a336aa;
  style 88a8e9ed-d92c-4340-aaad-c6d450a336aa stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Scaffolded assembly (fasta)
Input parameter Database for Kraken2

Outputs

From Output Label
Input parameter Database for Kraken2
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1 Kraken2 ID non-target contaminants
toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0 Parse mitochondrial blast parsing blast output
Filter1 Filter
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1 Concatenate datasets concatenate scaffold lists
toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 gfastats removing scaffolds

Tools

Tool Links
Cut1
Filter1
toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
3 8508dbeac 2024-09-03 19:00:32 format workflow and update test to the latest version of the workflow
2 eb3c5175f 2024-08-23 20:55:43 Simplify the workflow
1 72a8cb1ed 2024-08-16 16:20:33 creation of a tutorial for Asssembly decontamination'

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-decontamination/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows